[EMBOSS] Question about showalign program

[Linlin Yan]

K and E are treated similar because they are both charged, according
to the default matrix (EBLOSUM62), in which the score between K and E
is positive 1. Maybe you could use parameter -matrix to set your
specified score matrix.

On Thu, Oct 29, 2009 at 2:39 AM, Jean Mao <maoj at helix.nih.gov> wrote:
> Hi,
>
> A user of ours have a question regarding showaling. When running showalign
> with the input file (attached), the consensus (and parental) residue is
> Lysine (K) and one of her mutants residue is Glutamic acid (E). Lysine is
> basic and Glutamic acid is basic, which are opposites and shouldn't be
> similar. She was using all default setting which supposed to show (E) in the
> alignment output. But instead, it shows (e) which indicate similarity
> between Lysine and Glutamic acid. Can someone help?
>
> Thank you
>
> Jean Mao
>
>
>>A1
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSSQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD
>>A2
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>A3
> ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD
>>A4
> ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCEGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>A6
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLRASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>A7
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>A8
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARVLWFRDWGKMDVWGKGTTVTVSVD
>>A9
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQTPGKGLEWMGIIYPDGSDTRYGPSFQGQVTISFDKSIDTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>B1
> ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVS
>>B2
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>B4
> ASQMTQSPSSLSASVGDRVAITCRVSQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYNFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>B5
> ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>B6
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGAIYPDDSDTRYSPSFQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>C1
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSISTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVA
>>C3
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSA
>>C4
> ASQMTQSPSSLPASVGDRVTITRRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDSTLTISSLQPEDFATYYCLQDYTYPRTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD
>>C6
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>C8
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>D1
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTATYYCARALRFRDWGKMDVWGRGTTVTVSVD
>>D2
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>D3
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>D7
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>D8
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>D9
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKGPGESLKISCRGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD
>>E4
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD
>>E9
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>E11
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYAYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWLRDWGKMDVWGKGTTVTVSVD
>>F1
> ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD
>>F2
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>F3
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRTGARWTSGAKGPRSPSPS
>>F4
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSSTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>G1
> ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTRSPSP
>>G2
> QMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVS
>>G3
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>G4
> ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYGPSFRGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVPVD
>>G5
> ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAGVKKPGESLKISCKGSGYSFTDYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD
>>G6
> ASQMTQSPSSLSASVGGRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARASWFRDWGKMDVWGKGTTVTVSVD
>
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